conduitR

Overview

conduitR is an R package that provides tools for metaproteomics analysis using conduit and conduit-GUI. It offers a comprehensive suite of functions for processing, analyzing, and visualizing metaproteomics data. These functions are designed to be used in conjunction with the conduit and conduit-GUI packages, or independently for custom analyses.

Features

• Getting Data
  • Download FASTA files.
  • Download taxonomy data from NCBI
• Data Processing
  • Create custom protein sequence databases
  • Associate sample proteomics data and metadata using QFeatures integration.
  • Transformation, Imputation, and Normalization, of proteomics data.
• Statistical Analysis
  • Perform LIMMA differential expression analysis
  • Support for various machine learning models (LASSO, Random Forest, XGBoost)
  • Feature importance analysis
• Visualization

  • Interactive heatmaps with annotations

  • PCA biplots with customizable aesthetics

  • Taxonomic barplots

  • Taxonomic heat trees

  • Volcano plots for differential expression

  • KEGG pathway visualization

  • Feature-specific plots

  • Custom plot aesthetics

  • Miscellaneous

  • Logging functions.

Installation

You can install the development version of conduitR from GitHub:

r, eval = FALSE # install.packages("devtools") devtools::install_github("baynec2/conduitR")

Usage

This is a work in progress, will update in the future.